Related papers: SBtab - Conventions for structured data tables in …
Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
The demanding requirements of the new Big Data intensive era raised the need for flexible storage systems capable of handling huge volumes of unstructured data and of tackling the challenges that traditional databases were facing. NoSQL…
We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data.…
Structured data summarization involves generation of natural language summaries from structured input data. In this work, we consider summarizing structured data occurring in the form of tables as they are prevalent across a wide variety of…
We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on…
Synthetic data is often positioned as a solution to replace sensitive fixed-size datasets with a source of unlimited matching data, freed from privacy concerns. There has been much progress in synthetic data generation over the last decade,…
Recent standardization work for database languages has reflected the growing use of typed graph models (TGM) in application development. Such data models are frequently only used early in the design process, and not reflected directly in…
The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the…
Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the…
In an era of rapidly advancing data-driven applications, there is a growing demand for data in both research and practice. Synthetic data have emerged as an alternative when no real data is available (e.g., due to privacy regulations).…
Detecting synthetic tabular data is essential to prevent the distribution of false or manipulated datasets that could compromise data-driven decision-making. This study explores whether synthetic tabular data can be reliably identified ''in…
SNOMED Clinical Terms (SNOMED CT) is one of the most widespread ontologies in the life sciences, with more than 300,000 concepts and relationships, but is distributed with no associated software tools. In this paper we present MySNOM, a…
In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about…
Tabular data is common yet typically incomplete, small in volume, and access-restricted due to privacy concerns. Synthetic data generation offers potential solutions. Many metrics exist for evaluating the quality of synthetic tabular data;…
Urban Building Energy Modeling (UBEM) is a critical tool to provide quantitative analysis on building decarbonization, sustainability, building-to-grid integration, and renewable energy applications on city, regional, and national scales.…
Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular…
This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our…
Question-answering (QA) on hybrid scientific tabular and textual data deals with scientific information, and relies on complex numerical reasoning. In recent years, while tabular QA has seen rapid progress, understanding their robustness on…
There is a large number of online documents data sources available nowadays. The lack of structure and the differences between formats are the main difficulties to automatically extract information from them, which also has a negative…